TB-Profiler result

Run: ERR072083

Summary

Run ID: ERR072083

Sample name:

Date: 31-03-2023 09:11:21

Number of reads: 4129543

Percentage reads mapped: 99.73

Strain: lineage4.8

Drug-resistance: Pre-XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7521 p.Ala74Ser missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289253 c.-12T>C upstream_gene_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide, ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.29
PPE35 2169866 c.747G>C synonymous_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726151 c.-42T>C upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.37
folC 2747478 p.Thr41Pro missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4039729 p.Asp326Asn missense_variant 0.99
panD 4043905 p.Glu126Val missense_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.2
embC 4242425 p.Arg855Gly missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Asn missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0